I've been enjoying Rogues part 1 immensely (latest version) up to the Missing Pia quest.

When i release her (Pia) from the cage at the Academy Andrik Snyder aka Bearded Man is supposed to show up upon trying to leave the room, but the scene does not trigger and I can leave freely. Pia suggest talking to Alfons, even makes a comment upon returning to the hideout as "it's good to be home", but Alfons is "unresponsive", Nathan doesn't care as well. Is this a bug? Tried reloading, clearing override, no use. I was not confronted with any "blackmailed" quest and as far as I've gathered the "Spotted!" quest is irrelevant. How to trigger that scene? Any debug mode commands? I've searched the net extensively, are the walkthroughs available on the web out of date? Maybe I'm supposed to do something else? Please help, I can't stand the thought of missing out on this great module

I had a similar bug on a previous playthrough: it was because the char model for Andrik had been turned invisible by a hak I had added to the module, and it prevented the encounter that's supposed to take place when you leave to room to happen.

Is he visible when you look for him in the toolset? He should be in the lower right corner of "Academy, Teachers' Quarters".

Indeed, he was invisible when I opened the toolset (he is parked in a hidden room), then I cleared override folder and then he became visible (similar to hyath priests). Unfortunately, although clearing the override made him visible in the editor the encounter still was not triggered in-game. Tell me which HAK should I remove???

Unfortunately I didn't manage to make the encounter trigger in my game. It seems the changes you make to the override or the hakpak (but it seems it was the override in your case) are not taken into account into the savegame and you have to start a new game from scratch.